We demonstrate that the controlled self-assembly of DNA nanostructures can happen on electron beam lithographically patterned surfaces at lower energy. The fluorescent dye coupled amine modified DNA nanostructures were selectively attached to the patterned glass substrates. The optimized binding interaction between self-assembled DNA nanostructures occurred preferably at lower beam energy due to the attractive energy between the pattern and DNAs. Patterns containing self-assembled DNA molecules with dimensions as small as 2 nm in height and 68 nm in width have been successfully demonstrated. The periodicity in DNA self-assembly was observed. This technology of combination of "top-down" fabrication and "bottom-up" self-assembly may find use wherever there is a need to attach self-assembled DNA molecules in a nanometer scale patterned surface for various applications. (C) 2013 The Electrochemical Society. All rights reserved.